The SAM3U4E require the Network Control Model (NCM) to show his power instead of the Ethernet Control Model (ECM) that can only run the ATmega32U4. My understanding from the documents specification of ECM and NCM is that those two protocols share almost nothing in common: the framing and control are much complex in NCM . My conclusion is that there are two distinct projects.

However, ECM will work on the two processors, even if it will be slow compared to NCM. So I propose to first start with a simpler ECM protocol to see if the ethernet over USB feature take some interest from the Arduino users community. Maybe the few Mbps bandwidth of ECM will already satisfy a lot of them.

Thanks for the offer of the Due, but I think i't a bit too early at this stage because aside of you, nobody have showed interest in this feature yet. So I am not so motivated to start burning a lot of time alone on a high end implementation. For the high end projects I already use cheap ARM with Linux that have ethernet over USB, host and device.